| Variant ID: vg0810407609 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 10407609 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 117. )
TCTTCTAATCTGTATGGTAGGATGGTATACACTTTAATGTGATCCGAGTGGCTTTTCATAAAGCAGAGATGTTGGCCTACAGAACATCTTAGAAGGAACA[T/C]
ACCTATATGAGTCCGACTGCTAGTCACAGTCTATGAGATCTTGGTGATCTCTAGATACTCATGAAAAGGCCAGGAGTATGACTTATATGCTCCAAACAGA
TCTGTTTGGAGCATATAAGTCATACTCCTGGCCTTTTCATGAGTATCTAGAGATCACCAAGATCTCATAGACTGTGACTAGCAGTCGGACTCATATAGGT[A/G]
TGTTCCTTCTAAGATGTTCTGTAGGCCAACATCTCTGCTTTATGAAAAGCCACTCGGATCACATTAAAGTGTATACCATCCTACCATACAGATTAGAAGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.90% | 9.60% | 7.22% | 3.22% | NA |
| All Indica | 2759 | 88.60% | 6.70% | 4.60% | 0.11% | NA |
| All Japonica | 1512 | 76.50% | 4.20% | 11.18% | 8.13% | NA |
| Aus | 269 | 19.30% | 72.90% | 7.81% | 0.00% | NA |
| Indica I | 595 | 95.00% | 1.30% | 3.70% | 0.00% | NA |
| Indica II | 465 | 84.90% | 9.70% | 5.38% | 0.00% | NA |
| Indica III | 913 | 88.40% | 7.90% | 3.50% | 0.22% | NA |
| Indica Intermediate | 786 | 86.10% | 7.60% | 6.11% | 0.13% | NA |
| Temperate Japonica | 767 | 91.80% | 2.10% | 5.61% | 0.52% | NA |
| Tropical Japonica | 504 | 54.60% | 6.00% | 21.23% | 18.25% | NA |
| Japonica Intermediate | 241 | 73.90% | 7.10% | 7.88% | 11.20% | NA |
| VI/Aromatic | 96 | 61.50% | 4.20% | 13.54% | 20.83% | NA |
| Intermediate | 90 | 73.30% | 7.80% | 12.22% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0810407609 | T -> C | LOC_Os08g17000.1 | upstream_gene_variant ; 2484.0bp to feature; MODIFIER | silent_mutation | Average:31.947; most accessible tissue: Minghui63 young leaf, score: 48.378 | N | N | N | N |
| vg0810407609 | T -> C | LOC_Os08g16990.1 | downstream_gene_variant ; 318.0bp to feature; MODIFIER | silent_mutation | Average:31.947; most accessible tissue: Minghui63 young leaf, score: 48.378 | N | N | N | N |
| vg0810407609 | T -> C | LOC_Os08g16990-LOC_Os08g17000 | intergenic_region ; MODIFIER | silent_mutation | Average:31.947; most accessible tissue: Minghui63 young leaf, score: 48.378 | N | N | N | N |
| vg0810407609 | T -> DEL | N | N | silent_mutation | Average:31.947; most accessible tissue: Minghui63 young leaf, score: 48.378 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0810407609 | 1.58E-06 | 1.12E-07 | mr1109_2 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0810407609 | NA | 3.44E-06 | mr1149_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0810407609 | 3.95E-06 | 3.95E-06 | mr1466_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0810407609 | NA | 5.40E-06 | mr1617_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |